Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder.

One of the brilliant ideas of John Spence when he saw the first diffraction patterns from the Linac Coherent Light Source was that one could solve the crystallographic phase problem by utilising the intensities between Bragg peaks. Because these intensities are due to the Fourier transform of the shape of the crystal, the approach came to be known as "shape-transform phasing." Shape-transform phasing was developed over the next ten years and formed the basis for many other interesting ideas and pursuits. Here we describe the current best implementation of the original idea using a lattice occupancy formalism and show that certain types of crystal defects can also be modelled via this approach, allowing the molecular structure to be recovered from the additional information offered by the inter-Bragg intensities from these crystal defects.

A Metropolis Monte Carlo algorithm for merging single-particle diffraction intensities.

Single-particle imaging with X-ray free-electron lasers depends crucially on algorithms that merge large numbers of weak diffraction patterns despite missing measurements of parameters such as particle orientations. The expand-maximize-compress (EMC) algorithm is highly effective at merging single-particle diffraction patterns with missing orientation values, but most implementations exhaustively sample the space of missing parameters and may become computationally prohibitive as the number of degrees of freedom extends beyond orientation angles. This paper describes how the EMC algorithm can be modified to employ Metropolis Monte Carlo sampling rather than grid sampling, which may be favorable for reconstruction problems with more than three missing parameters. Using simulated data, this variant is compared with the standard EMC algorithm.

A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy.

We develop an algorithm capable of imaging a three-dimensional object given a collection of two-dimensional images of that object that are significantly influenced by the curvature of the Ewald sphere. These two-dimensional images cannot be approximated as projections of the object. Such an algorithm is useful in cryo-electron microscopy where larger samples, higher resolution, or lower energy electron beams are desired, all of which contribute to the significance of Ewald curvature.

Shape transform phasing of edgy nanocrystals.

Diffraction patterns from small protein crystals illuminated by highly coherent X-rays often contain measurable interference signals between Bragg peaks. This coherent `shape transform' signal introduces enough additional information to allow the molecular densities to be determined from the diffracted intensities directly, without prior information or resolution restrictions. However, the various correlations amongst molecular occupancies/vacancies at the crystal surface result in a subtle yet critical problem in shape transform phasing whereby the sublattices of symmetry-related molecules exhibit a form of partial coherence amongst lattice sites when an average is taken over many crystal patterns. Here an iterative phase retrieval algorithm is developed which is capable of treating this problem; it is demonstrated on simulated data.

Properties of Nuclei up to A=16 using Local Chiral Interactions.

We report accurate quantum Monte Carlo calculations of nuclei up to A=16 based on local chiral two- and three-nucleon interactions up to next-to-next-to-leading order. We examine the theoretical uncertainties associated with the chiral expansion and the cutoff in the theory, as well as the associated operator choices in the three-nucleon interactions. While in light nuclei the cutoff variation and systematic uncertainties are rather small, in ^{16}O these can be significant for large coordinate-space cutoffs. Overall, we show that chiral interactions constructed to reproduce properties of very light systems and nucleon-nucleon scattering give an excellent description of binding energies, charge radii, and form factors for all these nuclei, including open-shell systems in A=6 and 12.

Occupational exposure to ultrafine particles in police officers: no evidence for adverse respiratory effects.

BACKGROUND: Inhalation exposure to fine and ultrafine particles (UFPs) has been associated with respiratory diseases. However, little is known on the quality, threshold levels and concentration of these particles causing adverse health effects. METHODS: The impact of occupational exposure to submicrometer and UFPs was assessed in 30 healthy police shooting instructors by clinical investigation, self-assessment questionnaire, sputum and spirometry and compared to a control group. General laboratory chemistry parameters, circulating cytokines (interleukin [IL]-2, IL-4, IL-5, IL-6, IL-8, interferon-gamma [IFN-γ]), and granulocyte macrophage colony-stimulating factor (GM-CSF) in serum were measured. UFP exposure was recorded by Scanning Mobility Particle Sizer. RESULTS: Concentrations of submicrometer sized airborne particles (< 700 nm) measured between 3.34 × 105/cm3 and 7.58 × 105/cm3 at shooting sites, with highest concentrations found in the UFP range (< 100 nm). The size of the monodispersed particles ranged from 54.74 ± 16.25 nm to 98.19 ± 22.83 nm. Short term exposure (4 h) to high levels of UFPs caused an increase of IFN-γ in exposed subjects (p = 0.022). 24 h after exposure a significant decrease of IgG, albumin fibrinogen and factor VII was found. Neither directly after 4 h of high levels UFPs exposure nor 24 h after exposure subjective complaints or objective measurements indicating adverse respiratory effects in exposed subjects were found. CONCLUSIONS: No consistent indications for adverse respiratory or inflammatory effects directly following exposure and 24 h after exposure to high levels of UFPs in our study group were detected. However we showed the assessment of short-term exposure effects at a genuine occupational setting, which might is relevant when a risk assessment of high level occupational exposures to UFPs is considered.

Chiral Three-Nucleon Interactions in Light Nuclei, Neutron-α Scattering, and Neutron Matter.

We present quantum Monte Carlo calculations of light nuclei, neutron-α scattering, and neutron matter using local two- and three-nucleon (3N) interactions derived from chiral effective field theory up to next-to-next-to-leading order (N(2)LO). The two undetermined 3N low-energy couplings are fit to the (4)He binding energy and, for the first time, to the spin-orbit splitting in the neutron-α P-wave phase shifts. Furthermore, we investigate different choices of local 3N-operator structures and find that chiral interactions at N(2)LO are able to simultaneously reproduce the properties of A=3,4,5 systems and of neutron matter, in contrast to commonly used phenomenological 3N interactions.

Pattern motion representation in primary visual cortex is mediated by transcortical feedback.

A highly important question in visual neuroscience is to identify where in the visual system information from different processing channels is integrated to form the complex scenery we perceive. A common view to this question is that information is processed hierarchically because small and selective receptive fields in lower visual areas melt into larger receptive fields in specialized higher visual areas. However, a higher order area in which all incoming signals ultimately converge has not yet been identified. Rather, modulation of subthreshold influences from outside the classical receptive field related to contextual integration occurs already in early visual areas. So far it is unclear how these influences are mediated (Gilbert, 1998; Angelucci and Bullier, 2003; Gilbert and Sigman, 2007). In the present study, we show that feedback connections from a higher motion processing area critically influence the integration of subthreshold global motion cues in early visual areas. Global motion cues are theoretically not discernible for a local motion detector in V1, however, imprints of pattern motion have been observed in this area (Guo et al., 2004; Schmidt et al., 2006). By combining reversible thermal deactivation and optical imaging of intrinsic signals we demonstrate that feedback signals from the posteromedial suprasylvian sulcus are critical for the discrimination between global and local motions already in early visual areas. These results suggest that global features of the visual scenery are fed back to lower visual processing units in order to facilitate the integration of local cues into a global construct.

Heavy-light fermion mixtures at unitarity.

We investigate fermion pairing in the unitary regime for a mass ratio corresponding to a ;{6}Li-;{40}K mixture using quantum Monte Carlo methods. The ground-state energy and the average light- and heavy-particle excitation spectrum for the unpolarized superfluid state are nearly independent of the mass ratio. In the majority light system, the polarized superfluid is close to the energy of a phase separated mixture of nearly fully polarized normal and unpolarized superfluid. For a majority of heavy particles, we find an energy minimum for a normal state with a ratio of approximately 3ratio1 heavy to light particles. A slight increase in attraction to k_{F}a approximately 2.5 yields a ground state energy of nearly zero for this ratio. A cold unpolarized system in a harmonic trap at unitarity should phase separate into three regions, with a shell of unpolarized superfluid in the middle.

Tomographic femtosecond x-ray diffractive imaging.

A method is proposed for obtaining three simultaneous projections of a target from a single radiation pulse, which also allows the relative orientation of successive targets to be determined. The method has application to femtosecond x-ray diffraction, and does not require solution of the phase problem. We show that the principal axes of a compact charge-density distribution can be obtained from projections of its autocorrelation function, which is directly accessible in diffraction experiments. The results may have more general application to time resolved tomographic pump-probe experiments and time-series imaging.

Equation of state of superfluid neutron matter and the calculation of the 1S0 pairing gap.

We present a quantum Monte Carlo study of the zero-temperature equation of state of neutron matter and the computation of the 1S0 pairing gap in the low-density regime with rho < 0.04 fm(-3). The system is described by a nonrelativistic nuclear Hamiltonian including both two- and three-nucleon interactions of the Argonne and Urbana type. This model interaction provides very accurate results in the calculation of the binding energy of light nuclei. A suppression of the gap with respect to the pure BCS theory is found, but sensibly weaker than in other works that attempt to include polarization effects in an approximate way.

Auxiliary field diffusion Monte Carlo calculation of nuclei with A < or = 40 with tensor interactions.

We calculate the ground-state energy of (4)He, (8)He, (16)O, and (40)Ca using the auxiliary field diffusion Monte Carlo method in the fixed-phase approximation and the Argonne v(6)' interaction which includes a tensor force. Comparison of our light nuclei results to those of Green's function Monte Carlo calculations shows the accuracy of our method for both open and closed-shell nuclei. We also apply it to (16)O and (40)Ca to show that quantum Monte Carlo methods are now applicable to larger nuclei.

Pfaffian pairing wave functions in electronic-structure quantum Monte Carlo simulations.

We investigate the accuracy of trial wave functions for quantum Monte Carlo based on Pfaffian functional form with singlet and triplet pairing. Using a set of first row atoms and molecules we find that these wave functions provide very consistent and systematic behavior in recovering the correlation energies on the level of 95%. In order to get beyond this limit we explore the possibilities of multi-Pfaffian pairing wave functions. We show that a small number of Pfaffians recovers another large fraction of the missing correlation energy comparable to the larger-scale configuration interaction wave functions. We also find that Pfaffians lead to substantial improvements in fermion nodes when compared to Hartree-Fock wave functions.

Green's function Monte Carlo method with exact imaginary-time propagation.

We present a general formulation of the Green's function Monte Carlo method in imaginary-time quantum Monte Carlo which employs exact propagators. This algorithm has no time-step errors and is obtained by minimal modifications of the time-independent Green's function Monte Carlo method. We describe how the method can be applied to the many-body Schrödinger equation, lattice Hamiltonians, and simple field theories. Our modification of the Green's function Monte Carlo algorithm is applied to the ground state of liquid 4He. We calculate the zero-temperature imaginary-time diffusion constant and relate that to the effective mass of a mass-four "impurity" atom in liquid 4He.

Superfluid Fermi gases with large scattering length.

We report quantum Monte Carlo calculations of superfluid Fermi gases with short-range two-body attractive interactions with infinite scattering length. The energy of such gases is estimated to be (0.44+/-0.01) times that of the noninteracting gas, and their pairing gap is approximately twice the energy per particle.

Comparative endocrinology of the insulin-like growth factor-binding protein.

Emerging early in chordate evolution, the IGF-regulatory axis diverged from an insulin-like predecessor into a vertebrate regulatory system specializing in cell growth activation and allied anabolic functions. Essential to the divergence of the IGF and insulin systems was an early presence of soluble IGF-binding proteins (IGFBPs), which bind IGF peptides at much higher affinity than that of the insulin receptor but at comparable affinities to that of the IGF receptor. IGFBPs have no homology with IGF receptors. Instead, IGFBPs are a derived group of proteins within a superfamily of cysteine-rich growth factors, whose members are found throughout the animal taxa. While blocking IGF actions through the insulin receptor is a fundamental role, IGFBPs evolved within the vertebrate line into centralized, 'integrators' of the endocrine growth-regulatory apparatus. IGFBPs have substantial influences on the distribution and bioavailability of IGF peptides in the cellular and physiological environments, but they have a variety of other properties. The six principal mammalian IGFBPs exhibit an array of specialized properties that appear to be derived from a complex evolutionary history (including cell membrane association, interaction with proteins that post-translationally modify them, direct IGF-independent effects on cells, and others) and they are regulated by a diversity of 'outside' factors (e.g. other hormones, metabolic status, stress). Thus, IGFBPs are multifunctional integrators having diverse physiological 'agendas'. Much less is known about IGFBPs and their properties in the other vertebrate taxa. Increasingly, however, it is being recognized that they play equally important endocrine roles, in both conserved and non-conserved ways, when compared with those currently defined in mammals. This review highlights selected 'comparative aspects' in current IGFBP research, in an attempt to view this essential group of endocrine regulators from a wider, biological perspective.

Association between vitamin E and enhanced athletic performance in sled dogs.

PURPOSE: To determine the association between prerace plasma vitamin E concentration and performance in sled dogs competing in the 1998 Iditarod Race. METHODS: Prerace blood samples were collected from 670 dogs. Samples were analyzed for plasma vitamin E concentration while controlling for selected hematological and biochemical variables and signalment. Starting in teams of 16, exercise consisted of running up to 1159 miles pulling a laden sled and musher via checkpoints. The records of dogs that were withdrawn from the race for health reasons, fatigue, or strategic or technical reasons, and those of dogs that finished the race were analyzed. Multiple logistic regression and Cox proportional hazards analysis were used to determine factors associated with endurance. Multiple linear regression analysis was used to determine factors associated with team speed. RESULTS: A total of 323 dogs (48%) were withdrawn from racing at various distances from the start. Median time to finish for 39 teams was 11.5 d and the winning time was 9.2 d. Dogs with prerace plasma vitamin E concentrations > 40.7 microg.mL-1 were 1.9 times more likely to finish (P = 0.0006) and had 1.8 times less of a risk of being withdrawn for every mile ran (P = 0.03) than were dogs with plasma vitamin E concentrations between 16.3 and 40.7 microg.mL-1. Neither a team's mean prerace vitamin E concentration, nor the proportion of dogs within a team with high (> 40.7 microg.mL-1) vitamin E concentration was associated with team speed. CONCLUSIONS: Dogs with higher plasma vitamin E concentrations have enhanced endurance compared with dogs with lower plasma vitamin E concentrations, but the plasma vitamin E status of a team is not associated with team speed.

Vitamin E and exertional rhabdomyolysis during endurance sled dog racing.

Exertional rhabdomyolysis (ER) is common in sled dogs, animals with high energy expenditures that consume high fat (60% of ingested calories) diets. Associations between pre-race plasma [vitamin E] and total antioxidant status (TAS) and risk of developing ER were examined in dogs competing in the 1998 Iditarod race. Pre-race blood samples were collected from 750 dogs and a second sample was collected from 158 dogs withdrawn from the race at various times. Plasma creatine kinase activity was used to identify withdrawn dogs with ER. There was no association between pre-race plasma [vitamin E] and risk of development of ER. Dogs that developed ER started the race with higher TAS, but when withdrawn, had lower TAS than unaffected dogs and had similar pre-race [vitamin E] but higher [vitamin E] at time of withdrawal. Hence, the risk of ER in sled dogs is not affected by plasma [vitamin E] before the race.

Down-regulation in the insulin-like growth factor (IGF) axis during hibernation in the golden-mantled ground squirrel, Spermophilus lateralis: IGF-I and the IGF-binding proteins (IGFBPs).

The golden-mantled ground squirrel, Spermophilus lateralis, undergoes a profound winter hibernation that represents, among other changes, a prolonged period of starvation. In addition to dramatic metabolic and other physiological adaptations during hibernation which serve to reduce fuel energy expenditure, we have hypothesized that there may also be significant changes in the endocrine axis that regulates energetically-expensive somatic growth. As compared with euthermic, non-hibernating controls, hibernating S. lateralis were found to have 75%-reduced serum concentrations of insulin-like growth factor-I (IGF-I; from approximately 625 to approximately 150 ng/ml in both females and males, P < 0.05). While IGFBP-3 was the predominant IGFBP in serum of the euthermic controls, its levels were reduced to a similar degree in serum from the hibernating animals. IGFBP-4 was present at relatively low levels in the euthermic controls, and was reduced to undetectable levels in hibernating animals. Surprisingly, there was no IGFBP detectable in the 30 kDa range in either euthermic or hibernating S. lateralis, suggesting that IGFBP-1 does not play a role in hibernation-related changes in the IGF axis. In accordance with these endocrine changes, when serum from hibernating S. lateralis was added to cartilage explant cultures (at a 5% v/v concentration), it exhibited no ability to alter (35)S-proteoglycan synthetic rate, whereas serum from the euthermic squirrels significantly stimulated synthetic activity by 2-fold. These results suggest that part of hibernation adaptation in S. lateralis includes down-regulation in the growth-regulatory IGF axis. J. Exp. Zool. 289:66-73, 2001.

Matching the modules: cortical maps and long-range intrinsic connections in visual cortex during development.

Visual cortical neurons exhibit a high degree of response selectivity and are grouped into small columns according to their response preferences. The columns are located at regularly spaced intervals covering the whole cortical representation of the visual field with a modular system of feature-selective neurons. The selectivity of these cells and their modular arrangement is thought to emerge from interactions in the network of specific intracortical and thalamocortical connections. Understanding the ontogenesis of this complex structure and contributions of intrinsic and extrinsic, experience-dependent mechanisms during cortical development can provide new insights into the way the visual cortex processes information about the environment. Available data about the development of connections and response properties in the visual cortex suggest that maturation proceeds in two distinct steps. In the first phase, mechanisms inherent to the cortex establish a crude framework of interconnected neural modules which exhibit the basic but still immature traits of the adult state. Relevant mechanisms in this phase are assumed to consist of molecular cues and patterns of spontaneous neural activity in cortical and corticothalamic interconnections. In a second phase, the primordial layout becomes refined under the control of visual experience establishing a fine-tuned network of connections and mature response properties.